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- PDB-2bis: Structure of glycogen synthase from Pyrococcus abyssi -

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Basic information

Entry
Database: PDB / ID: 2bis
TitleStructure of glycogen synthase from Pyrococcus abyssi
ComponentsGLGA GLYCOGEN SYNTHASE
KeywordsTRANSFERASE / GLYCOSYLTRANSFERASE FAMILY / 5 UDP/ADP-GLUCOSE-GLYCOGEN SYNTHASE / TWO ROSSMAN FOLDS
Function / homology
Function and homology information


glycogen (starch) synthase activity / nucleotide binding
Similarity search - Function
Glycosyl transferases group 1 / Bacterial/plant glycogen synthase / Starch synthase, catalytic domain / Starch synthase catalytic domain / Glycosyl transferases group 1 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / alpha-D-glucopyranose / URIDINE-5'-DIPHOSPHATE / Glycogen synthase
Similarity search - Component
Biological speciesPYROCOCCUS ABYSSI (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHorcajada, C. / Guinovart, J.J. / Fita, I. / Ferrer, J.C.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Crystal Structure of an Archaeal Glycogen Synthase: Insights Into Oligomerisation and Substrate Binding of Eukaryotic Glycogen Synthases.
Authors: Horcajada, C. / Guinovart, J.J. / Fita, I. / Ferrer, J.C.
History
DepositionJan 25, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLGA GLYCOGEN SYNTHASE
B: GLGA GLYCOGEN SYNTHASE
C: GLGA GLYCOGEN SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,27623
Polymers147,9863
Non-polymers2,29020
Water0
1
A: GLGA GLYCOGEN SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1379
Polymers49,3291
Non-polymers8098
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: GLGA GLYCOGEN SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8697
Polymers49,3291
Non-polymers5416
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: GLGA GLYCOGEN SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2697
Polymers49,3291
Non-polymers9416
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)202.985, 73.973, 148.221
Angle α, β, γ (deg.)90.00, 131.19, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12A
22B
32C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A1 - 11
2115B1 - 11
3115C1 - 11
1215A13 - 45
2215B13 - 45
3215C13 - 45
1315A55 - 151
2315B55 - 151
3315C55 - 151
1415A153 - 169
2415B153 - 169
3415C153 - 169
1515A174 - 217
2515B174 - 217
3515C174 - 217
1615A414 - 437
2615B414 - 437
3615C414 - 437
1125A218 - 294
2125B218 - 294
3125C218 - 294
1225A305 - 314
2225B305 - 314
3225C305 - 314
1325A317 - 337
2325B317 - 337
3325C317 - 337
1425A339 - 392
2425B339 - 392
3425C339 - 392
1525A396 - 413
2525B396 - 413
3525C396 - 413

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.245, -0.97, -0.007), (0.462, -0.123, 0.878), (-0.852, 0.212, 0.478)0.72676, -1.05238, 0.73308
2given(-0.32012, 0.44008, -0.83896), (-0.9454, -0.20558, 0.2529), (-0.06118, 0.87411, 0.48186)0.77712, 0.58377, 0.29646

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Components

#1: Protein GLGA GLYCOGEN SYNTHASE


Mass: 49328.551 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROCOCCUS ABYSSI (archaea) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): (DE3)-RIL
References: UniProt: Q9V2J8, starch synthase (glycosyl-transferring)
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE / 1,4-Dioxane


Mass: 88.105 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H8O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 0.55 %
Crystal growpH: 5.6 / Details: pH 5.60

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.8→29.5 Å / Num. obs: 41024 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.1
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.878 / SU ML: 0.296 / Cross valid method: THROUGHOUT / ESU R Free: 0.395 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.266 2060 5 %RANDOM
Rwork0.2 ---
obs0.204 38891 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å20 Å2-1.22 Å2
2--0.75 Å20 Å2
3----1.17 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10449 0 132 0 10581
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02210808
X-RAY DIFFRACTIONr_bond_other_d0.0050.0210038
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.97414542
X-RAY DIFFRACTIONr_angle_other_deg0.814323284
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.08251315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.57323.133482
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.624151860
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0491574
X-RAY DIFFRACTIONr_chiral_restr0.0780.21567
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211875
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022352
X-RAY DIFFRACTIONr_nbd_refined0.2110.22305
X-RAY DIFFRACTIONr_nbd_other0.1970.210217
X-RAY DIFFRACTIONr_nbtor_refined0.1870.25209
X-RAY DIFFRACTIONr_nbtor_other0.0910.26185
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2237
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2030.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6931.56660
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.925210426
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.34934679
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0394.54116
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1326medium positional0.190.5
12B1326medium positional0.170.5
13C1326medium positional0.190.5
21A1057medium positional0.290.5
22B1057medium positional0.340.5
23C1057medium positional0.320.5
11A2192loose positional0.515
12B2192loose positional0.545
13C2192loose positional0.565
21A1682loose positional0.765
22B1682loose positional0.735
23C1682loose positional0.835
11A1326medium thermal0.772
12B1326medium thermal0.522
13C1326medium thermal0.662
21A1057medium thermal1.142
22B1057medium thermal0.882
23C1057medium thermal1.692
11A2192loose thermal1.4410
12B2192loose thermal1.210
13C2192loose thermal1.2910
21A1682loose thermal1.9410
22B1682loose thermal1.9510
23C1682loose thermal2.9910
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.394 134
Rwork0.296 2822

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